All publications and patent applications herein are incorporated by reference, fully as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
Various strategies for finding solutions to mathematical problems have been devised which use sets of DNA oligonucleotides having selected length and sequence properties. For example, DNA-based methods are developed for solving a Hamiltonian path problem (Adleman, Science, 1994, Vol. 266, pages 1021-3), a "satisfaction" problem (Lipton, Science, 1995, Vol. 268, pages 542-5), and for performing addition (Guarnieri et al., 1996, Science, vol. 273, pages 220-223) and matrix multiplication (Oliver, J. Molecular Evolution, 1997, Vol. 45, pages 161-7 ) of non-negative numbers. Each computation requires a set of oligonucleotides having properties tailored to the problem to be solved. Thus, a rapid and efficient method for providing custom sets of oligonucleotides having selected sequence and length properties is essential for efficient application of DNA-based computation methods.
The present ability to detect oligonucleotides that are bound in a sequence-specific manner to discrete sites of a hybridization array permits the use of oligonucleotides to encrypt and transmit data; a use which, like nucleic acid computation, requires numerous custom sets of oligonucleotides having particular sequences and hybridization properties.
Oligonucleotides are also used as hybridization probes to detect specific nucleic acid sequences in DNA and RNA samples immobilized on a variety of filter and solid supports, as in DNA and RNA Dot, Southern, and Northern blots, and in colony and plaque hybridization assays. These methodologies are widely used in the isolation and cloning of specific nucleic acids, and the diagnosis of disease caused by pathogens and genetic mutations (Berent et al., BioTechniques, issue of May/June 1985, pages 208-20; and J. Sambrook, E. F. Fritsch, and T. Maniatis, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989, Chapter 11). After detection of labeled probes on a hybridization filter, it is a common practice to expose the hybridization filter to denaturing conditions such as solution of low ionic strength and high temperature, in order to wash the hybridizing probe molecules from the filter, making the filter ready for re-hybridization with a different hybridization probe (Protocols for DNA and RNA Transfer, DNA Electrotransfer, and Protein Transfer to Biodyne A Nylon Membranes, Pall Ultrafine Filtration Corporation, East Hills, N.Y., 1985, page 14).
Sets of oligonucleotides of defined sequence are used as primers for polymerases in polynucleotide synthesis and in nucleic acid amplification, for example, by the polymerase chain reaction (PCR, see Erlich, PCR Technology, Stockton Press, New York, 1989, in entirety). Sets of oligonucleotides of defined sequence are also used as probes of macromolecular structure, and are screened to identify oligomers which, either as antisense or as triplex-forming oligonucleotides, bind specifically to a native target nucleic acid such as a folded mRNA molecule (see, for example, Milner et al., Nature Biotechnology, 1987, Vol. 15, pages 537-41; and U.S. Pat. No. 5,176,996).
More recently, oligonucleotides have been immobilized or synthesized in micro-arrays on solid supports of material such as glass or SiO.sub.2. "DNA chips" produced in this manner are useful for detecting or capturing multiple nucleic acid targets, for determining the nucleic type sequence of a target nucleic acid, for simultaneous analysis of the expression of thousands of genes, large scale gene discovery, DNA polymorphism screening, and mapping of genomic DNA clones, and are well suited for use in medical diagnostic assays for detection of pathogen infection and genetic mutation (for example, see U.S. Pat. No. 5,445,934; U.S. Pat. No. 5,503,980; U.S. Pat. No. 5,605,662; Caviani-Pease et al., 1994, PNAS, Vol. 91, pages 5022-6; and reviews by Ramsay, 1998, Nature Biotechnology, Vol. 16, pages 40-44; and Marshall et al., 1998, Nature Biotechnology, Vol. 16, pages 27-31).
Fodor et al. (U.S. Pat. No. 5,445,934, col. 3-21, 23-32) describes photolithographic solid-phase synthesis of arrays of oligomers, including arrays of oligonucleotides of known nucleotide sequence. The oligomer arrays are synthesized on a substrate by attaching photo-removable groups to the surface of a substrate, exposing selected regions of the substrate to light to activate those regions, and attaching monomeric subunits with photo-removable groups to the activated regions. The steps of photo-activation and attachment can be repeated until oligomers of desired length and sequence are synthesized. According to the current state of the art pertaining to the photolithographic synthesis of polynucleotide arrays, there is only a 92-94% chance that a new nucleotide will be incorporated where desired (McGall et al., J. Am. Chem. Soc., 1997, vol. 119, pages 5081-90). Current technology thus imposes certain constraints on the possible array configuration, such as a practical upper limit on the number of nucleotides of approximately ten.
McGall et al. (U.S. Pat. No. 5,412,087, col. 4-20) describes substrates with surfaces to which are attached compounds having a thiol functional group protected by a photo-removable protecting group, which compounds can be used to construct arrays of immobilized anti-ligands, such as oligonucleotide probes.
Heller et al. describe a "master" DNA chip comprising a controllable, integrated array of micro-electrodes, and teaches denaturing double-stranded complexes comprising oligonucleotides at selected sites by increasing the negative potential and by use of chemical denaturants, in a process in which the oligomers hybridized at the selected sites are transferred to, or "printed" onto, another chip (U.S. Pat. No. 5,605,662, col. 20, lines 16-39).
DNA oligonucleotides of defined sequence can also be used as structural components of an electronic computer chip (Hollenberg et al., U.S. Pat. No. 5,561,071).
As is apparent from the preceding discussion there are numerous computational, data transmission-related, molecular biological, biochemical, and diagnostic applications which require the use of sets of oligonucleotides or oligonucleotide analogs of defined sequence and length. There currently is a need for a method for rapidly and efficiently providing the various combinations of oligomers required for applications such as those discussed above.